recursionpharma/nesso ? reverse-engineered prompt

Build me a Python tool called Nesso that can predict binding affinity for a protein and ligand pair from a simple YAML file. I want to be able to give it a protein sequence, a ligand SMILES string, and an affinity target, then run one command and get a prediction plus an output folder with the results.

Please make it work nicely from the command line, with a clear predict command, support for reading the YAML input, and sensible defaults so it works on CPU but can also use a GPU if available. If there are optional speedups that only work in some setups, make them optional and easy to turn off. Include a small example input and a short tutorial so I can try it right away.

Also add tests, basic docs, and make the project easy to install from source. If you need to check current dependency or install details, look them up online.